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- PDB-6a3a: MVM NES mutant Nm2 in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 6a3a
TitleMVM NES mutant Nm2 in complex with CRM1-Ran-RanBP1
Components
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • MVM NES mutant Nm2
  • Ran-specific GTPase-activating protein 1
KeywordsTRANSPORT PROTEIN / nuclear export / complex / mutant / inhibitor
Function / homology
Function and homology information


exit of virus from host cell nucleus through nuclear pore / Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / RNA nuclear export complex / pre-miRNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear export signal receptor activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / manchette ...exit of virus from host cell nucleus through nuclear pore / Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / RNA nuclear export complex / pre-miRNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear export signal receptor activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / protein localization to kinetochore / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / nuclear export / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / spindle pole body / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / NLS-bearing protein import into nucleus / MAPK6/MAPK4 signaling / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / viral process / mRNA export from nucleus / U2 snRNA binding / U6 snRNA binding / ribosomal subunit export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / U1 snRNA binding / protein export from nucleus / centriole / GTPase activator activity / mitotic spindle organization / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / recycling endosome / G protein activity / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / G1/S transition of mitotic cell cycle / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / actin cytoskeleton organization / midbody / ubiquitin-dependent protein catabolic process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / host cell nucleus / chromatin / nucleolus / GTP binding / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal ...Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Ran binding domain / Ran binding protein RanBP1-like / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Non-structural protein NS2 / Exportin-1 / Ran-specific GTPase-activating protein 1 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
Minute virus of mice
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSun, Q. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)81502629 China
CitationJournal: Int J Nanomedicine / Year: 2021
Title: Cancer Therapy with Nanoparticle-Medicated Intracellular Expression of Peptide CRM1-Inhibitor.
Authors: Sui, M. / Xiong, M. / Li, Y. / Zhou, Q. / Shen, X. / Jia, D. / Gou, M. / Sun, Q.
History
DepositionJun 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: Ran-specific GTPase-activating protein 1
C: Exportin-1
D: MVM NES mutant Nm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,8449
Polymers160,1204
Non-polymers7255
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-57 kcal/mol
Surface area58720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.650, 106.650, 304.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-1265-

HOH

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 26404.184 Da / Num. of mol.: 1 / Mutation: Y197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62826
#2: Protein Ran-specific GTPase-activating protein 1 / Chromosome stability protein 20 / Perinuclear array-localized protein / Ran-binding protein 1 / RANBP1


Mass: 16521.867 Da / Num. of mol.: 1 / Fragment: Ran Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Plasmid: pGEX4t-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41920
#3: Protein Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 115052.273 Da / Num. of mol.: 1 / Fragment: lacking C-terminal inhibitory tail and H9 loop
Mutation: D537G, T539C, V540E, K541Q, Y1022C, 377-413 deletion, 441-461 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGEX4t-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30822

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide MVM NES mutant Nm2


Mass: 2141.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Minute virus of mice / Gene: NS2 / Plasmid: pGEX4t-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0DJZ2*PLUS

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Non-polymers , 6 types, 269 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.54 % / Mosaicity: 0.324 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 18% PEG3350, 200mM Ammonium Nitrate, 100mM Bis-Tris pH6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 78675 / % possible obs: 99.6 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.045 / Rrim(I) all: 0.125 / Χ2: 0.662 / Net I/σ(I): 2.8 / Num. measured all: 972120
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.3-2.3412.738430.330.8670.52899
2.34-2.3812.638300.370.7510.52198.9
2.38-2.4312.538690.4610.6630.51498.9
2.43-2.4812.538460.5220.5680.53699
2.48-2.5312.338190.6180.4630.51599.3
2.53-2.5911.838810.7150.3990.52799.5
2.59-2.6611.738610.7520.340.5399.1
2.66-2.7312.638830.8430.2650.53999.50.930.968
2.73-2.8112.639010.8750.2170.54999.40.7640.795
2.81-2.912.638720.9170.1760.55899.70.6160.641
2.9-312.438900.9490.1390.56899.80.4820.502
3-3.1212.139360.9660.1070.59899.80.3650.381
3.12-3.2611.539270.9770.0840.63799.80.2790.291
3.26-3.4412.639370.9880.0590.66599.80.2060.215
3.44-3.6512.739480.9910.0440.7331000.1540.16
3.65-3.9312.739750.9940.0350.83199.90.120.125
3.93-4.3311.939970.9960.030.9861000.10.104
4.33-4.9513.240280.9960.0251.0631000.0880.092
4.95-6.2412.440880.9960.0250.8851000.0850.088
6.24-5011.743440.9970.020.88299.90.0650.068

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HAT

4hat


Resolution: 2.3→33.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 24.276 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 4019 5.1 %RANDOM
Rwork0.2091 ---
obs0.2111 74398 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 159.22 Å2 / Biso mean: 70.759 Å2 / Biso min: 40.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.84 Å2
Refinement stepCycle: final / Resolution: 2.3→33.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10902 0 44 264 11210
Biso mean--69.19 62.81 -
Num. residues----1352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01411171
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710315
X-RAY DIFFRACTIONr_angle_refined_deg0.9421.65415111
X-RAY DIFFRACTIONr_angle_other_deg0.7741.63624141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93651347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44623.713571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.864152050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1561550
X-RAY DIFFRACTIONr_chiral_restr0.0450.21482
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212254
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022042
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 288 -
Rwork0.362 5356 -
all-5644 -
obs--98.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2271.0389-0.94332.9369-0.83493.2168-0.02280.2833-0.0438-0.15270.101-0.4984-0.17230.3273-0.07810.10220.02010.01170.2796-0.09260.13157.7-5.15432.724
21.34590.28110.53572.26732.36666.5524-0.1312-0.00680.1285-0.05030.0495-0.0808-0.62950.51740.08180.4033-0.18470.09760.44940.00650.212460.56817.18119.818
30.5721-0.20440.09880.88230.11411.08540.01750.0259-0.0640.0430.0455-0.21580.02130.036-0.06310.1079-0.0448-0.01060.2079-0.03030.078340.434-15.35630.949
419.23568.9225-2.485614.5686-2.05746.14180.082-0.43630.57760.3135-0.00280.6597-0.3628-0.3455-0.07920.40090.12460.00340.2735-0.01340.034114.90922.98929.049
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 303
2X-RAY DIFFRACTION2B64 - 200
3X-RAY DIFFRACTION3C-1 - 1052
4X-RAY DIFFRACTION4D77 - 93

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